Thanks, folks! Everything you've said has clarified many things, and I'm
working on putting them into practice. But in the meantime, I've got a new
error condition, with the same repositories (and complex repository
dependencies), and could use some guidance.
I started to see this error condition when I removed the toolshed and
changeset_revision tags in the tool_dependencies.xml for the dependent
repository xena_install. It now reads:
<?xml version="1.0"?>
<tool_dependency>
<package name="installXena" version="1.0">
<repository name="start_xena" owner="melissacline"/>
</package>
</tool_dependency>
Short and simple. But lately, when I try to install this repository from
the test toolshed, I get a pop-up window from Chrome (my web browser) that
says "The page at 127.0.0.1:8080 says:", "Initializing repository
installation failed", with an OK button. There is no error message visible
in paster.log. Here is what I do see:
127.0.0.1 - - [12/Sep/2014:11:45:57 -0700] "GET
/admin_toolshed/prepare_for_ins\
tall?tool_shed_url=
https://testtoolshed.g2.bx.psu.edu/&repository_ids=4ab1d3705\
ad0de2d&changeset_revisions=fe95cf1ae864 HTTP/1.1" 200 - "-"
"Mozilla/5.0
(Maci\
ntosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/37.\
0.2062.94 Safari/537.36"
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
\
DEBUG 2014-09-12 11:46:05,937 Creating repository dependency objects...
tool_shed.util.shed_util_common DEBUG 2014-09-12 11:46:07,214 Updating an
exist\
ing row for repository 'xena_import' in the tool_shed_repository table,
status \
set to 'New'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
\
DEBUG 2014-09-12 11:46:07,241 Skipping installation of revision
75c7d80df9c1 of\
repository 'start_xena' because it was installed with the (possibly
updated) r\
evision 75c7d80df9c1 and its current installation status is 'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
\
DEBUG 2014-09-12 11:46:07,241 Building repository dependency
relationships...
127.0.0.1 - - [12/Sep/2014:11:46:05 -0700] "POST
/admin_toolshed/prepare_for_in\
stall HTTP/1.1" 200 - "
http://127.0.0.1:8080/admin_toolshed/prepare_for_install\
?tool_shed_url=
https://testtoolshed.g2.bx.psu.edu/&repository_ids=4ab1d3705ad0d\
e2d&changeset_revisions=fe95cf1ae864" "Mozilla/5.0 (Macintosh; Intel Mac OS
X 1\
0_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94
Safari/537.36\
"
warning:
testtoolshed.g2.bx.psu.edu certificate with fingerprint
79:94:82:1f:74\
:e6:f8:5c:1c:b8:3e:8d:89:f0:0e:88:9a:ac:2b:61 not verified (check
hostfingerpri\
nts or web.cacerts config setting)
127.0.0.1 - - [12/Sep/2014:11:46:07 -0700] "POST
/admin_toolshed/manage_reposit\
ories HTTP/1.1" 500 - "
http://127.0.0.1:8080/admin_toolshed/prepare_for_install\
" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36
(KHTML, li\
ke Gecko) Chrome/37.0.2062.94 Safari/537.36"
Debug at:
http://127.0.0.1:8080/_debug/view/1410547505
Then when I click OK, the status of the tool changes to "Cloning", and
stays in that state indefinitely while paster.log keeps logging a repeat of
this message:
127.0.0.1 - - [12/Sep/2014:11:55:28 -0700] "POST
/admin_toolshed/repository_ins\
tallation_status_updates HTTP/1.1" 200 - "
http://127.0.0.1:8080/admin_toolshed/\
prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4)
AppleWebKi\
t/537.36 (KHTML, like Gecko) Chrome/37.0.2062.94 Safari/537.36"
Just in case this is from some cruft from a previous installation, I tried
starting over with a brand new galaxy-dist directory. It doesn't look like
that changed anything.
Any ideas? Many thanks in advance!
Melissa
On Fri, Sep 12, 2014 at 10:30 AM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Melissa,
The revision recorded in the filesystem path can seem odd at first glance.
My inline responses should hopefully clarify that.
--Dave B.
On 09/10/2014 05:49 PM, Melissa Cline wrote:
> Hi Folks,
>
> Okay, I really need debugging ideas on this one.
>
> I have three repositories I'm developing under the test toolshed.
> They're named start_xena, xena_import and xena_find_datasets (they're
> all under visualization). start_xena contains a simple tool dependency
> to a package named installXena. xena_import and xena_find_datasets
> contain complex dependencies to installXena. I've installed these tools
> on two computers. On one, everything works great - amazingly well, in
> fact! Kudos, Development Team! On the other computer, the env.sh files
> associated with the complex dependencies keep referencing the wrong
> version of start_xena/installXena.
>
> Here are the gory details.
>
> The start_xena tool is installed in
>
testtoolshed.g2.bx.psu.edu/repos/melissacline/start_xena/
> 82755b0ee5a5/start_xena
> <
http://testtoolshed.g2.bx.psu.edu/repos/melissacline/
> start_xena/82755b0ee5a5/start_xena>.
> I'm a bit confused about the revision part of the path, because the
> latest revision is different (75c7d80df9c1), and I have uninstalled and
> re-installed the tool since its last update. Its package, installXena,
> is installed under tool_dependencies at
> tool_dependencies/installXena/1.0/melissacline/start_xena/82755b0ee5a5/.
> That directory contains all the files I'd expect to be there, and its
> env.sh file contains all the environment variables I'd intended to set.
> So far, so good.
>
> xena_import is installed on my computer at
>
testtoolshed.g2.bx.psu.edu/repos/melissacline/xena_
> import/dc42b6bbc22b/xena_import
> <
http://testtoolshed.g2.bx.psu.edu/repos/melissacline/
> xena_import/dc42b6bbc22b/xena_import>.
> Its tool_dependencies.xml reference installXena under start_xena as:
>
> <?xml version="1.0"?>
>
> <tool_dependency>
>
> <package name="installXena" version="1.0">
>
> <repository toolshed="http://testtoolshed.g2.bx.psu.edu"
> name="start_xena" owner="melissacline" changeset_revision="
> 82755b0ee5a5"/>
>
> </package>
>
> </tool_dependency>
>
> (Aside: is it necessary to have the changeset_revision in there? I'm a
> bit worried about the maintenance task of updating it for all of my
> dependent tools every time I update start_xena, but as I'll explain,
> it's not clear that this revision info is getting used).
>
It is not necessary to populate the changeset_revision or toolshed
attributes. If you omit them, they will be automatically filled in based on
the most recent matching repository.
> The tool dependency dir for xena_import is at
> tool_dependencies/installXena/1.0/melissacline/xena_import/dc42b6bbc22b/.
> Its
> env.sh reads:
>
> if [ -f
> /Users/melissacline/src/galaxy-dist/tool_dependencies/
> installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
> ] ; then .
> /Users/melissacline/src/galaxy-dist/tool_dependencies/
> installXena/1.0/melissacline/start_xena/0676a227dbc6/env.sh
> ; fi
>
> Notice that the wrong revision number is in there. The 06 revision was
> an older one. Needless to say, the files and environment variables I
> need aren't in the 06 directory.
>
> Where does this incorrect revision number come from? I've deleted all
> the 06 directories, repeatedly. I've deleted and reinstalled the tools,
> and verified that after deletion, the directories in question were in
> fact gone. I've tried resetting the metadata for these tools under the
> Galaxy Admin menu. Now I need new ideas. As I mentioned, all of this
> works beautifully on a second computer. It's as if the first Galaxy
> installation, on the first computer, got stuck with some outdated
> information, and I haven't figured out how to clear it out.
>
The 0676 revision number is based on the revision that was first
installed, and should never change. When you update the repository, the
database will record the new revision in a separate field, but the original
revision id needs to be recorded in order to find the env.sh file on the
filesystem.
> Thanks!
>
> Melissa
>
>
>
>
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